Dependency and Expression Embedding Figures
Neekesh Dharia & Guillaume Kugener
2020-08-18
Generated using: 20Q1
The table below highlights all of the cell lines that are included in the analyses and the types that they are annotated as:
Overview
- Embed the pediatric and adult solid and brain tumor cell lines in expression/dependency space
- Evaluate homogeneity in expression/dependency space
Expression 2D embedding
Global all cell line expression 2D embedding
Only the top 2000 most variable genes were selected to perform the 2D embedding
tSNE
UMAP
Pediatric cell line expression 2D embedding
Only the top 2000 most variable genes across pediatric cell lines were selected to perform the 2D embedding
tSNE
tSNE with labels
UMAP
UMAP with labels
Dependency 2D embedding
Global (all DepMap cell lines) embedding
Embedding of cell lines in dependency space only using the selective dependencies (LRT > 100, exclude common essentals, exclude non-essentials, exclude genes with NAs):
509, 656 genes
tSNE
UMAP
UMAP - color only peds
tSNE - color tumor types
UMAP - color tumor types
Interactive plot
Pediatric cell line dependency 2D embedding
All selective dependecies (across pediatric and adult solid/brain tumors) across pediatric cell lines were used to perform the 2D embedding
tSNE
tSNE with labels
UMAP
UMAP with labels
Measuring cell line similarity
Here we generate similarity scores between cell lines and then assess the similarity scores.
Correlation: calculate the pairwise correlation for all cell lines across the top 2000 or 500 most variable genes (expression or dependency, respectively).
Repeated k-means: repeated k-means approach and repeatedly cluster cell lines using kmeans. The similiarity score is the fraction of times that two cell lines cluster with one another.
Distance to cluster center in post PCA: run PCA on expression or dependency space and then select the number of PCs that explain the most variabce using the elbow method. For each lineage, set the center of the lineage cluster to be the median of each of the PCs for cell lines in that lineage. Then calculate the average distance of each cell line to the center and plot.
Only tumor types that have >= 3 cell lines are included in this analysis. The black dashed line indicates the median similarity with cell lines not within that tumor type.
Correlations
Repeated kmeans
Distance to center in PCA
Expression
On the top 2000 most variable genes.
Dependency
LRT genes only
Below, we plot the median distance from the cluster center in expression and dependency and then fit a line using the geom_smooth function.
Top 500 genes only
Below, we plot the median distance from the cluster center in expression and dependency and then fit a line using the geom_smooth function.
Session Info
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.2 (2019-12-12)
## os macOS Catalina 10.15.6
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-08-18
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
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##
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